Index

_

_align_motifs_with_clustalo() (trviz.motif_aligner.MotifAligner static method) _align_motifs_with_mafft() (trviz.motif_aligner.MotifAligner static method) _align_motifs_with_muscle() (trviz.motif_aligner.MotifAligner static method) _build_repeat_finder_hmm() (trviz.decomposer.Decomposer static method) _calculate_cost() (in module trviz.utils)

_decompose_dp() (trviz.decomposer.Decomposer static method) _decompose_hmm() (trviz.decomposer.Decomposer method) _divide_motifs_into_normal_and_private() (trviz.motif_encoder.MotifEncoder static method) _encode_decomposed_tr() (trviz.motif_encoder.MotifEncoder static method) _get_motif_aligner() (trviz.motif_aligner.MotifAligner method) _get_unique_labels() (trviz.visualizer.TandemRepeatVisualizer static method)

A

add_dendrogram() (trviz.visualizer.TandemRepeatVisualizer method)

add_padding() (in module trviz.utils) align() (trviz.motif_aligner.MotifAligner method)

C

calculate_cost() (in module trviz.utils)

calculate_cost_with_dist_matrix() (in module trviz.utils) calculate_total_cost() (in module trviz.utils)

D

decompose() (trviz.decomposer.Decomposer method) Decomposer (class in trviz.decomposer)

DIGITS (in module trviz.utils) DNA_CHARACTERS (in module trviz.utils)

E

encode() (trviz.motif_encoder.MotifEncoder method)

encode_tr_sequence() (trviz.visualizer.TandemRepeatVisualizer static method)

F

find_private_motif_threshold() (trviz.motif_encoder.MotifEncoder static method)

G

generate_trplot() (trviz.main.TandemRepeatVizWorker method) get_distance_matrix() (in module trviz.utils) get_levenshtein_distance() (in module trviz.utils) get_motif_counter() (in module trviz.utils) get_motifs_from_visited_states_and_region() (in module trviz.utils)

get_population_colormap() (trviz.visualizer.TandemRepeatVisualizer method) get_repeating_pattern_lengths() (in module trviz.utils) get_sample_and_sequence_from_fasta() (in module trviz.utils) get_score_matrix() (in module trviz.utils) get_symbol_to_color_map() (trviz.visualizer.TandemRepeatVisualizer static method)

I

INDEX_TO_CHR (in module trviz.utils)

is_emitting_state() (in module trviz.utils) is_valid_sequence() (in module trviz.utils)

L

load_aligned_trs() (trviz.motif_aligner.MotifAligner static method)

LOWERCASE_LETTERS (in module trviz.utils)

M

module trviz trviz.decomposer trviz.main trviz.motif_aligner trviz.motif_encoder trviz.utils trviz.visualizer

MotifAligner (class in trviz.motif_aligner) MotifEncoder (class in trviz.motif_encoder)

P

plot_motif_color_map() (trviz.visualizer.TandemRepeatVisualizer static method)

print_progress_bar() (in module trviz.utils) PRIVATE_MOTIF_LABEL (in module trviz.utils)

S

set_symbol_to_color_map() (trviz.visualizer.TandemRepeatVisualizer method) skipping_characters (in module trviz.utils)

sort() (in module trviz.utils) sort_by_manually() (in module trviz.utils) sort_by_simulated_annealing_optimized() (in module trviz.utils)

T

TandemRepeatVisualizer (class in trviz.visualizer) TandemRepeatVizWorker (class in trviz.main) trplot() (trviz.visualizer.TandemRepeatVisualizer method) trviz module trviz.decomposer module trviz.main module

trviz.motif_aligner module trviz.motif_encoder module trviz.utils module trviz.visualizer module

U

UPPERCASE_LETTERS (in module trviz.utils)

W

write_motif_map() (trviz.motif_encoder.MotifEncoder static method)